merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index e7e1aa77a49005f553c2657271a7d1ecd6dbac12..9a71a038cd4d0bd29d7eaeeeaae96d9847d81fa8 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -37,14 +37,14 @@ LibShuffCommand::LibShuffCommand(string option){
                        string Array[] =  {"iters","groups","step","form","cutoff"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
-                       parser = new OptionParser();
-                       parser->parse(option, parameters);  delete parser;
+                       OptionParser parser(option);
+                       map<string, string> parameters = parser.getParameters();
                        
-                       ValidParameters* validParameter = new ValidParameters();
+                       ValidParameters validParameter;
                
                        //check to make sure all parameters are valid for command
-                       for (it = parameters.begin(); it != parameters.end(); it++) { 
-                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
                        //make sure the user has already run the read.dist command
@@ -54,7 +54,7 @@ LibShuffCommand::LibShuffCommand(string option){
                                                
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       groups = validParameter->validFile(parameters, "groups", false);                        
+                       groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; savegroups = groups; }
                        else { 
                                savegroups = groups;
@@ -63,18 +63,16 @@ LibShuffCommand::LibShuffCommand(string option){
                        }
                                
                        string temp;
-                       temp = validParameter->validFile(parameters, "iters", false);                           if (temp == "not found") { temp = "10000"; }
+                       temp = validParameter.validFile(parameters, "iters", false);                            if (temp == "not found") { temp = "10000"; }
                        convert(temp, iters); 
                        
-                       temp = validParameter->validFile(parameters, "cutoff", false);                          if (temp == "not found") { temp = "1.0"; }
+                       temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "1.0"; }
                        convert(temp, cutOff); 
                        
-                       temp = validParameter->validFile(parameters, "step", false);                            if (temp == "not found") { temp = "0.01"; }
+                       temp = validParameter.validFile(parameters, "step", false);                             if (temp == "not found") { temp = "0.01"; }
                        convert(temp, step); 
        
-                       userform = validParameter->validFile(parameters, "form", false);                        if (userform == "not found") { userform = "integral"; }
-                       
-                       delete validParameter;
+                       userform = validParameter.validFile(parameters, "form", false);                 if (userform == "not found") { userform = "integral"; }
                        
                        if (abort == false) {